A Beretta 92F/FS is seen with Tokyo Army Criminal Investigation Division officers.
Daewoo K5
The Daewoo K5 is seen with Takehisa Hinawa in "Mind Blown".
Heckler & Koch USP
The Heckler & Koch USP is seen with Takehisa, showing in the OP sequence, "SPARK-AGAIN".
M1911A1
The M1911A1 returns in the seasons as Takehisa's sidearm.
Submachine Guns
Minebea PM-9
The Minebea PM-9 is used by Takehisa as his main submachine gun in the season.
Rifles
Howa Type 89
The Howa Type 89 was used by most of Special Fire Force Company 2 as their primary weapon.
Hybrid rifle
Hinawa is seen to be using a hybrid rifle that's based on a Double rifle with some parts taken from the Tanegashima, first seen in the OP sequence "Torch of Liberty".
Shotguns
Ithaca 37
An Ithaca 37 appears to be used by Takehisa to fire buckshot rounds powered by his Fire Soldier powers in "A Fire Soldier's Fight".
Machine Guns
M134 Minigun
Juggernaut creates two flaming miniguns when he faces Orochi in the abandoned Tokyo Metro subways in "Weapons of Destruction".
Rocket Launchers
Saab Bofors Dynamics AT4
A Saab Bofors Dynamics AT4 appears to be use in "A Fire Soldier's Fight". The sound effects used in the episode makes it sound like the AT4 is configured as a multi-shot grenade launcher.
Grenades
Extinguisher Grenade
The Extinguisher grenades return from the first season, being used as a non-lethal weapon to subdue flames or a distraction device against Infernals since tossing one makes smoke.